Merge pull request #15 from OGGM/oggm-dev

No more deprecation warnings

docs/INSTALL.rst

@@ -38,6 +38,7 @@ I/O:
 
 GIS and geometrical tools:
     - gdal
+    - rasterio
     - shapely
     - pyproj
     - geopandas

docs/install_virtualenv.rst

@@ -111,7 +111,7 @@ Details: http://tylerickson.blogspot.co.at/2011/09/installing-gdal-in-python-vir
 
 Install further stuffs::
 
-    $ pip install pyproj Pillow geopandas netcdf4 scikit-image configobj joblib
+    $ pip install pyproj rasterio Pillow geopandas netcdf4 scikit-image configobj joblib
 
 And the external libraries::
 

oggm/prepro/centerlines.py

@@ -33,6 +33,7 @@
 # Locals
 import oggm.conf as cfg
 from salem import lazy_property
+from oggm.utils import tuple2int
 
 # Module logger
 log = logging.getLogger(__name__)
@@ -452,9 +453,9 @@ def compute_centerlines(gdir, div_id=None):
     nc.close()
 
     # Find for local maximas on the outline
+    x, y = tuple2int(poly_pix.exterior.xy)
     ext_yx = tuple(reversed(poly_pix.exterior.xy))
-    ext_yx = (ext_yx[0][:-1], ext_yx[1][:-1])  # last point is first point
-    zoutline = topo[ext_yx]
+    zoutline = topo[y[:-1], x[:-1]]  # last point is first point
 
     # Size of the half window to use to look for local maximas
     maxorder = np.rint(cfg.params['localmax_window'] / gdir.grid.dx)
@@ -495,12 +496,12 @@ def compute_centerlines(gdir, div_id=None):
     costgrid = _make_costgrid(glacier_mask, glacier_ext, topo)
 
     # Terminus
-    t_coord = np.asarray(ext_yx)[:, np.argmin(zoutline)]
+    t_coord = np.asarray(ext_yx)[:, np.argmin(zoutline)].astype(np.int64)
 
     # Compute the routes
     lines = []
     for h in heads:
-        h_coord = np.asarray(h.xy)[::-1]
+        h_coord = np.asarray(h.xy)[::-1].astype(np.int64)
         indices, _ = route_through_array(costgrid, h_coord, t_coord)
         lines.append(shpg.LineString(np.array(indices)[:, [1, 0]]))
     log.debug('%s: computed the routes', gdir.rgi_id)
@@ -562,8 +563,8 @@ def compute_downstream_lines(gdir):
         topo = nc.variables['topo_smoothed'][:]
 
     # Variables we gonna need
-    xmesh, ymesh = np.meshgrid(np.arange(0, gdir.grid.nx, 1),
-                               np.arange(0, gdir.grid.ny, 1))
+    xmesh, ymesh = np.meshgrid(np.arange(0, gdir.grid.nx, 1, dtype=np.int64),
+                               np.arange(0, gdir.grid.ny, 1, dtype=np.int64))
     _h = [topo[:, 0], topo[0, :], topo[:, -1], topo[-1, :]]
     _x = [xmesh[:, 0], xmesh[0, :], xmesh[:, -1], xmesh[-1, :]]
     _y = [ymesh[:, 0], ymesh[0, :], ymesh[:, -1], ymesh[-1, :]]
@@ -574,8 +575,8 @@ def compute_downstream_lines(gdir):
     div_ids = list(gdir.divide_ids)
     for div_id in div_ids:
         head = gdir.read_pickle('centerlines', div_id=div_id)[-1].tail
-        heigts.append(topo[head.y, head.x])
-        heads.append((head.y, head.x))
+        heigts.append(topo[int(head.y), int(head.x)])
+        heads.append((int(head.y), int(head.x)))
 
     # Now the lowest first
     aso = np.argsort(heigts)

oggm/prepro/climate.py

@@ -113,10 +113,14 @@ def mb_climate_on_height(gdir, heights, time_range=None, year_range=None):
     time = netCDF4.num2date(time[:], time.units)
     if time_range is not None:
         p0 = np.where(time == time_range[0])[0]
-        if len(p0) == 0:
+        try:
+            p0 = p0[0]
+        except IndexError:
             raise RuntimeError('time_range[0] not found in file')
         p1 = np.where(time == time_range[1])[0]
-        if len(p1) == 0:
+        try:
+            p1 = p1[0]
+        except IndexError:
             raise RuntimeError('time_range[1] not found in file')
     else:
         p0 = 0

oggm/prepro/geometry.py

@@ -35,6 +35,7 @@
 import oggm.conf as cfg
 from oggm import utils
 import oggm.prepro.centerlines
+from oggm.utils import tuple2int
 
 # Module logger
 log = logging.getLogger(__name__)
@@ -467,7 +468,7 @@ def catchment_area(gdir, div_id=None):
     cost_factor = 0.  # Make it cheap
     dic_catch = dict()
     for i, cl in enumerate(cls):
-        x, y = cl.line.xy
+        x, y = tuple2int(cl.line.xy)
         costgrid[y, x] *= cost_factor
         for x, y in [(int(x), int(y)) for x, y in cl.line.coords]:
             assert (y, x) not in dic_catch
@@ -477,11 +478,11 @@ def catchment_area(gdir, div_id=None):
     computed = np.where(mask == 1, 0, np.nan)
 
     # Coords of Terminus
-    endcoords = np.array(cls[0].tail.coords[0])[::-1]
+    endcoords = np.array(cls[0].tail.coords[0])[::-1].astype(np.int64)
 
     # Start with all the paths at the boundaries, they are more likely
     # to cover much of the glacier
-    for headx, heady in glacier_pix.exterior.coords:
+    for headx, heady in tuple2int(glacier_pix.exterior.coords):
         indices, _ = route_through_array(costgrid, np.array([heady, headx]),
                                          endcoords)
         inds = np.array(indices).T
@@ -498,7 +499,7 @@ def catchment_area(gdir, div_id=None):
         not_computed = np.where(computed == 0)
         if len(not_computed[0]) == 0:  # All points computed !!
             break
-        headcoords = np.array([not_computed[0][0], not_computed[1][0]])
+        headcoords = np.array([not_computed[0][0], not_computed[1][0]]).astype(np.int64)
         indices, _ = route_through_array(costgrid, headcoords, endcoords)
         inds = np.array(indices).T
         computed[inds[0], inds[1]] = 1
@@ -678,8 +679,8 @@ def catchment_width_geom(gdir, div_id=None):
 
         # Filter +- widths at junction points
         for fid in fl.inflow_indices:
-            i0 = np.clip(fid-jpix, jpix/2, n-jpix/2)
-            i1 = np.clip(fid+jpix+1, jpix/2, n-jpix/2)
+            i0 = np.clip(fid-jpix, jpix/2, n-jpix/2).astype(np.int64)
+            i1 = np.clip(fid+jpix+1, jpix/2, n-jpix/2).astype(np.int64)
             widths[i0:i1] = np.NaN
 
         valid = np.where(np.isfinite(widths))

oggm/prepro/gis.py

@@ -25,9 +25,9 @@
 from shutil import copyfile
 from functools import partial
 # External libs
-import osr
+from osgeo import osr
 import salem
-import gdal
+from osgeo import gdal
 import pyproj
 import numpy as np
 import shapely.ops
@@ -38,11 +38,12 @@
 from scipy.ndimage.measurements import label
 # Locals
 import oggm.conf as cfg
+from oggm.utils import tuple2int
 
 # Module logger
 log = logging.getLogger(__name__)
 
-# Variable needed later
+# Needed later
 label_struct = np.ones((3, 3))
 
 
@@ -205,12 +206,12 @@ def proj(x, y):
     (x, y) = glacier_poly_pix.exterior.xy
     glacier_mask[skdraw.polygon(np.array(y), np.array(x))] = 1
     for gint in glacier_poly_pix.interiors:
-        x, y = gint.xy
-        glacier_mask[skdraw.polygon(np.array(y), np.array(x))] = 0
+        x, y = tuple2int(gint.xy)
+        glacier_mask[skdraw.polygon(y, x)] = 0
         glacier_mask[y, x] = 0  # on the nunataks, no
-    ext_yx = tuple(reversed(glacier_poly_pix.exterior.xy))
-    glacier_mask[ext_yx] = 1
-    glacier_ext[ext_yx] = 1
+    x, y = tuple2int(glacier_poly_pix.exterior.xy)
+    glacier_mask[y, x] = 1
+    glacier_ext[y, x] = 1
 
     # Because of the 0 values at nunataks boundaries, some "Ice Islands"
     # can happen within nunataks (e.g.: RGI40-11.00062)

oggm/tests/test_graphics.py

@@ -1,12 +1,9 @@
 from __future__ import division
 
-from nose.tools import assert_true
+import warnings
+warnings.filterwarnings("once", category=DeprecationWarning)
 
 import os
-import sys
-import copy
-import shutil
-import warnings
 from six.moves.urllib.request import urlopen
 from six.moves.urllib.error import URLError
 

oggm/tests/test_prepro.py

@@ -1,27 +1,26 @@
 from __future__ import absolute_import, division
 
+import warnings
+warnings.filterwarnings("once", category=DeprecationWarning) # , module=r'.*oggm.*'
+
 import unittest
 import os
-import sys
-import pickle
 
 import shapely.geometry as shpg
 import numpy as np
 import shutil
 import pandas as pd
 import geopandas as gpd
-import matplotlib.pyplot as plt
 import netCDF4
-import multiprocessing as mp
 
 # Local imports
 from oggm.prepro import gis, centerlines, geometry, climate, inversion
 import oggm.conf as cfg
 from oggm.utils import get_demo_file
 from oggm import utils
-import logging
 from xml.dom import minidom
 import salem
+from oggm.utils import tuple2int
 
 # Globals
 current_dir = os.path.dirname(os.path.abspath(__file__))
@@ -107,7 +106,6 @@ def test_glacier_masks(self):
         np.testing.assert_allclose(area,gdir.glacier_area, rtol=1e-1)
         nc.close()
 
-
 class TestCenterlines(unittest.TestCase):
 
     def setUp(self):
@@ -211,8 +209,8 @@ def test_baltoro_centerlines(self):
         my_mask = np.zeros((gdir.grid.ny, gdir.grid.nx), dtype=np.uint8)
         cls = gdir.read_pickle('centerlines', div_id=1)
         for cl in cls:
-            ext_yx = tuple(reversed(cl.line.xy))
-            my_mask[ext_yx] = 1
+            x, y = tuple2int(cl.line.xy)
+            my_mask[y, x] = 1
 
         # Transform
         kien_mask = np.zeros((gdir.grid.ny, gdir.grid.nx), dtype=np.uint8)
@@ -240,8 +238,8 @@ def proj(x, y):
 
             kgm = transform(project, kgm)
 
-            ext_yx = tuple(reversed(kgm.xy))
-            kien_mask[ext_yx] = 1
+            x, y = tuple2int(kgm.xy)
+            kien_mask[y, x] = 1
 
         # We test the Heidke Skill score of our predictions
         rest = kien_mask + 2 * my_mask

oggm/tests/test_utils.py

@@ -1,5 +1,6 @@
 from __future__ import division
-
+import warnings
+warnings.filterwarnings("once", category=DeprecationWarning)
 import unittest
 import os
 

oggm/tests/test_workflow.py

@@ -1,5 +1,6 @@
 from __future__ import division
-
+import warnings
+warnings.filterwarnings("once", category=DeprecationWarning)
 import os
 import logging
 import shutil

oggm/utils.py

@@ -12,6 +12,7 @@
 import shutil
 import zipfile
 import sys
+from functools import partial
 
 # External libs
 import numpy as np
@@ -42,6 +43,8 @@
                                7.86570726e-01, 1.06450772e-01,
                                2.63865083e-04])
 
+tuple2int = partial(np.array, dtype=np.int64)
+
 
 def empty_cache():  # pragma: no cover
     """Empty oggm's cache directory."""